prepare_susie_data_with_torus_result: Prepare summary statistics with TORUS SNP-level priors as...

In kevinlkx/mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Prepare summary statistics with TORUS SNP-level priors as input data for SuSiE

Description

Check for required columns in summary statistics and adds TORUS SNP-level priors to summary statistics to be used as input data for susie_rss.

Usage

prepare_susie_data_with_torus_result(
  sumstats,
  torus_prior,
  torus_fdr = NULL,
  filter = c("none", "pval", "torus_fdr"),
  fdr.thresh = 0.1,
  pval.thresh = 5e-08
)

Arguments

sumstats	A data frame of summary statistics
torus_prior	A data frame with SNP level priors (result from run_torus() with option=“est-prior”)
torus_fdr	A data frame containing the FDR of each region (result from run_torus() with option=“fdr”). Optional, if available, only keep the loci with FDR < fdr.thresh.
filter	filter SNPs from sumstats: 'none': do not filter SNPs, 'pval': filter SNPs with GWAS pval < pval.thresh, 'torus_fdr': filter SNPs with TORUS FDR < torus_fdr.
fdr.thresh	FDR cutoff (default: 0.1)
pval.thresh	GWAS pval cutoff (default: 5e-8)

Value

A data frame of summary statistics with SNP-level priors to be used as input data for finemapping with SuSiE.

kevinlkx/mapgen documentation built on March 31, 2024, 11:03 p.m.